Clinical Molecular Diagnostic Laboratory (CMDL)
The Clinical Molecular Diagnostic Laboratory (CMDL) at the City of Hope® National Medical Center provides the medical and research communities with timely, accurate, high-quality molecular genetic testing, with expert interpretation and clinical consultation, through the delivery of excellent customer service, exemplary laboratory and clinical practices, and continual innovation in our processes.
CMDL is certified under the Clinical Laboratory Improvements Amendments of 1988 (CLIA ID No. 05D2302026), licensed by the State of California (CDF 90012253), and accreditation pending by the College of American Pathologists.
- Molecular Hematopathology
- Molecular Oncology
- Molecular Viral Testing
In addition to the services listed, we welcome proposals for candidate gene analyses. We offer a comprehensive molecular analysis of the regions of likely functional significance in the gene in cases and controls. The output is the enumeration of all sequence variants including a detailed analysis of the likelihood that each variant is of functional significance.
Molecular Hematopathology
HopeSeq Heme Comprehensive
Mutations (full exon of 523 genes), copy number variations (CNV), tumor mutation burden (TMB), gene fusions (>5,000 selected rearrangements in 165 genes) and expression (71 genes).
AML Rapid Genomics Assay
- Mutation analysis in the following genes: ASXL1, BCOR, BRAF, CALR, CEBPA, CSF3R, EZH2, FLT3, HRAS, IDH1, IDH2, JAK2 (exons 12-15), KIT, KRAS, MPL, MYD88, NPM1, NRAS, RUNX1, SETBP1, SF3B1, SRSF2, STAG2, TP53 (all exons), U2AF1, ZRSR2
- Quantitative RT PCR analysis of the following translocations: RUNX1::RUNXT1, CBFB::MYH11, BCR::ABL1, PML::RARA
Individual Molecular Testing for Hematologic Malignancies - BCR/ABL1 Kinase Mutation Analysis by NGS
- CALR Mutation Analysis
- CEBPA Mutation Analysis
- FLT3 Mutation Analysis, with ITD signal ratio
- IDH1 and IDH2 Mutation Analysis
- JAK2 Mutation Analysis
- KIT Mutation Analysis
Gene Rearrangement Assays
- IGH and IGK gene arrangements by PCR
- IGHV hypermutation analysis by NGS
- TCR-ϒ and TCR-β gene rearrangements by NGS
Quantitative RT-PCR Assays
- BCR/ABL translocation (t(9;22))
p190 BCR/ABL
p210 BCR/ABL (reporting on International Scale) - CBFB/MYH11 translocation (inv(16))
- Minimal Residual Disease (MRD) NPM1 Known Mutations
- PML/RARA translocation (t(15;17))
- RUNX1/RUNX1T1 translocation (t(8;21))
- MPL Mutation Analysis
- NPM1 Mutation Analysis
- TP53
Specimen Types
- HopeSeq Heme Comprehensive Panel: Blood, Bone Marrow Aspirate and FFPE
- AML Rapid Genomic Assay: Blood and Bone Marrow Aspirate
Individual Molecular Heme Testing: Blood, Bone Marrow Aspirate and FFPE - Quantitative RT-PCR Assays: Blood and Bone Marrow Aspirate
- Gene Rearrangement Assays: Blood, Bone Marrow Aspirate and FFPE
Specimen Requirements
- Blood: EDTA; 3 ml minimum, 6ml preferred.
- Bone Marrow Aspirate: EDTA; 3 ml minimum, 6ml preferred.
- FFPE: (Formalin Fixed Parrafin Embedded) Block with the highest tumor content, which is not exposed to any decalcifying solutions OR 1 H&E and 20 USS (unstained slides 4uM thickness)
Shipping/Handling
- Blood and Bone Marrow Aspirate: ship at ambient temperature if delivered on the same day, ship refrigerated otherwise. Do not freeze.
- FFPE: ship at ambient temperature.
Molecular Oncology
HopeSeq Solid Tumors Comprehensive
Mutations (full exon of 523 genes), CNV, microsatellite instability (MSI), TMB, gene fusion (>5,000 selected rearrangements in 165 genes) and PD-L1 IHC (upon request).
HopeSeq Glioma Comprehensive
Mutations (full exon of 523 genes), CNV, MSI, TMB, gene fusion (>5,000 selected rearrangements in 165 genes), MGMT methylation analysis and PD-L1 IHC.
HopeSeq FNA Comprehensive (Lung, Thyroid, Upper GI)
Mutations (full exon of 523 genes), CNV MSI, TMB, gene fusion (>5,000 selected rearrangements in 165 genes). Expression of ephithelial markers will be evaluated for specimen sufficiency prior to NGS testing. Gene expression assay will be performed for adequacy assessment of FNA samples for this panel.
Individual Molecular Oncology Testing
- MGMT promoter methylation
- MLH1 gene, Methylation Analysis
Specimen Types
- HopeSeq Solid Tumors Comprehensive Panels: FFPE
- HopeSeq FNA Comprehensive Panel (Lung, Thyroid, Upper GI): FNA
- Individual Molecular Oncology Testing: FFPE
Specimen Requirements
- FFPE (Formalin Fixed Parrafin Embedded) Block with the highest tumor content, which is not exposed to any decalcifying solutions OR 1 H&E and 20 USS (unstained slides 4uM thickness)
- FNA (Fine Needle aspirations): Special DNA/RNA stabilizer tube will be provided. Call Lab Outreach for special transport tube instruction sheet before performing FNA.
Shipping/Handling
FFPE: ship at ambient temperature.
Molecular Genetics
HopeSeq Germline Confirmatory Panel
This panel confirms the presence of any suspicious cancer predisposition/germline alterations identified by HopeSeq Heme and Solid Tumor panels.
Specimen Types
- Cancer Predisposition (Hereditary) Panels: Blood
- Inherited Bleeding Disorders: Blood, Cultured Cells (Amniocentesis or Chorionic Villi Sampling)
Specimen Requirements
- Blood: EDTA; 3 ml minimum, 5ml preferred.
- Cultured cells: two Confluent T25 Flasks in medium.
Shipping/Handling
- Blood specimens: ship at ambient temperature if delivered on the same day, ship refrigerated otherwise. Do not freeze.
- Cultured cells: Ship ambient by overnight courier to arrive at the lab within 24 hr. Send padded to arrive on M/Tu/W.
Clinical Molecular Diagnostic Laboratory Faculty
Dr. Afkhami is a professor of molecular genomic pathology and hematopathology, CLIA director of Clinical Molecular Genomics and Cytogenomics laboratory, and division chief of molecular pathology and therapy biomarkers at City of Hope Comprehensive Cancer Center.
Milhan Telatar, Ph.D., is director of the Clinical Molecular Diagnostic Laboratory, an associate clinical professor in the Division of Molecular Pathology and Therapy Biomarkers and a clinical molecular geneticist in the Department of Pathology.
Javier Arias-Stella, M.D., is a surgical pathologist and molecular pathologist in the Department of Pathology at City of Hope.
Olga Danilova, M.D., Ph.D., is a pathologist in the Department of Pathology at City of Hope.
Raju Pillai, M.D., is a hematopathologist and molecular pathologist in the Department of Pathology at City of Hope.
Fei Fei, M.D., is an Assistant Clinical Professor in the Department of Pathology, specializing in molecular pathology.